[gmx-users] mdrun with mpich

[Pradeep Kota]

Thank you for your response Mr.David. I compiled lam successfully without
fortran support. all i wanted to know was whether it would make any
difference to the running time of gromacs. I am curious because, it is
well-known that fortran loops are faster than loops of other languages..so,
i wanted to clarify ! moreover, i would want to know how different this is,
from mpich.
thanks for the support.
regards,
kota.

On 2/2/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> Pradeep Kota wrote:
> > Thank you for your response, itamar..but the cluster isolated from the
> > internet for security reasons. i dont think there is any chance to use
> > fink on the head node either. any other alternatives?
> > regards,
>
> compile LAM without fortran, there's a flag for it
>
> > kota.
> >
> > On 2/2/06, *Itamar Kass* <ikass at cc.huji.ac.il
> > <mailto:ikass at cc.huji.ac.il> > wrote:
> >
> >     Why not using fortan?
> >     install it using Fink and let lam have it.
> >
> >        Itamar.
> >
> >     ===========================================
> >     | Itamar Kass
> >     | The Alexander Silberman
> >     | Institute of Life Sciences
> >     | Department of Biological Chemistry
> >     | The Hebrew University, Givat-Ram
> >     | Jerusalem, 91904, Israel
> >     | Tel: +972-(0)2-6585194
> >     | Fax: +972-(0)2-6584329
> >     | Email: ikass at cc.huji.ac.il <mailto:ikass at cc.huji.ac.il>
> >     | Net:
> >     http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html
> >     <http://www.ls.huji.ac.il/%7Emembranelab/itamar/itamar_homepage.html
> >
> >     ============================================
> >
> >         ----- Original Message -----
> >         *From:* Pradeep Kota <mailto:kotanmd at gmail.com>
> >         *To:* Discussion list for GROMACS users
> >         <mailto:gmx-users at gromacs.org>
> >         *Sent:* Thursday, February 02, 2006 4:43 AM
> >         *Subject:* [gmx-users] mdrun with mpich
> >
> >         Dear users,
> >             I have compiled gromacs on our dual core mac os x G5
> >         cluster, and tried running a simulation on a 540 residue protein
> >         for 1 ns on 8 processors. i used mpich as the mpi environment
> >         for parallelising gromacs. it worked fine, and the job was split
> >         properly and assigned to nodes. now, the cpu usage per processor
> >         is not more than 50% on any of the processors. and the total
> >         running time for this was 13hrs. though output is written
> >         properly onto the specified output file, mdirun doesnot
> >         terminate even after running through all the steps. it still
> >         shows two mdrun_mpi processes running on the head node, with a
> >         0% cpu usage. was going through gmx-users mailing list and
> >         somehow figured out that mpich is not a good idea for running
> >         gromacs. so, i wanted to switch over to lam. now when i complie
> >         gromacs using lam, it is not able to link the libraries
> >         properly. so, i tried reinstalling lam on my cluster. now, lam
> >         keeps complaining about not being able to find a fortran
> >         compiler. i should not need a fortran compiler unless i'm using
> >         SUN or SGI for this purpose..(am i going wrong here?). what
> >         flags do i need to compile lam with, in order to compile gromacs
> >         successfully? any help is very much appreciated..
> >         thanks in advance,
> >         regards,
> >         kota.
> >
> >
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>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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